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root/OpenMD/trunk/src/applications/staticProps/RadialDistrFunc.hpp

Comparing trunk/src/applications/staticProps/RadialDistrFunc.hpp (file contents):
Revision 307 by tim, Wed Feb 9 18:12:47 2005 UTC vs.
Revision 2023 by gezelter, Thu Oct 2 14:35:14 2014 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#ifndef APPLICATIONS_STATICPROPS_RADIALDISTRFUNC_HPP
43		#define APPLICATIONS_STATICPROPS_RADIALDISTRFUNC_HPP
#	Line 46 | Line 47
47
48		#include "selection/SelectionEvaluator.hpp"
49		#include "selection/SelectionManager.hpp"
50	<	namespace oopse {
50	>	#include "utils/NumericConstant.hpp"
51	>	#include "applications/staticProps/StaticAnalyser.hpp"
52
53	<	/**
52	<	* @class RadialDistrFunc
53	<	* @brief Radial Distribution Function
54	<	*/
55	<	class RadialDistrFunc {
56	<	public:
57	<	RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2. double len);
53	>	namespace OpenMD {
54
55	<	void process();
55	>	/**
56	>	* @class RadialDistrFunc
57	>	* @brief Radial Distribution Function
58	>	*/
59	>	class RadialDistrFunc : public StaticAnalyser {
60	>	public:
61	>	RadialDistrFunc(SimInfo* info, const std::string& filename,
62	>	const std::string& sele1, const std::string& sele2);
63
64	<	void setNBins(int nbins) {
62	<	assert(nbins > 0);
63	<	nbins_ = nbins;
64	<	delta_ = len_ / nbins_;
65	<	}
66	<
67	<	int getNBins() {
68	<	return nbins_;
69	<	}
64	>	virtual ~RadialDistrFunc() {}
65
66	<	void setOutputName(const std::string& filename) {
72	<	outputFilename_ = filename;
73	<	}
66	>	void process();
67
75	–	const std::string& getOutputFileName() const {
76	–	return outputFilename_;
77	–	}
68
79	–	void setStep(int step) {
80	–	assert(step > 0);
81	–	step_ =step;
82	–	}
69
70	<	protected:
70	>	protected:
71
72	<	virtual void preProcess() {}
73	<	virtual void postProcess() {}
72	>	virtual void preProcess() {}
73	>	virtual void postProcess() {}
74	>	virtual void processNonOverlapping(SelectionManager& sman1,
75	>	SelectionManager& sman2);
76	>	virtual void processOverlapping(SelectionManager& sman);
77
78	<	SimInfo* info_;
79	<	Snapshot* currentSnapshot_;
80	<	double len_;
92	<	int nbins_;
93	<	double delta_;
94	<	std::string dumpFilename_;
95	<	std::string outputFilename_;
96	<	int step_;
97	<	std::string selectionScript1_;
98	<	std::string selectionScript2_;
99	<	int nProcessed_;
100	<	private:
78	>	int getNPairs() { return nPairs_;}
79	>
80	>	Snapshot* currentSnapshot_;
81
82	<	virtual void initalizeHistogram() {}
83	<	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2) =0;
84	<	virtual void processHistogram() = 0;
82	>	std::string selectionScript1_;
83	>	std::string selectionScript2_;
84	>	int nProcessed_;
85	>	SelectionEvaluator evaluator1_;
86	>	SelectionEvaluator evaluator2_;
87
88	<	virtual void writeRdf() = 0;
88	>	SelectionManager seleMan1_;
89	>	SelectionManager seleMan2_;
90	>	SelectionManager sele1_minus_common_;
91	>	SelectionManager sele2_minus_common_;
92	>	SelectionManager common_;
93	>
94	>	private:
95
96	+	virtual void initializeHistogram() {}
97	+	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2) =0;
98	+	virtual void processHistogram() {}
99	+
100	+	virtual void validateSelection1(SelectionManager& sman) {}
101	+	virtual void validateSelection2(SelectionManager& sman) {}
102	+	virtual void writeRdf() = 0;
103
104	<	SelectionEvaluator evaluator1_;
105	<	SelectionEvaluator evaluator2_;
111	<	SelectionManager seleMan1_;
112	<	SelectionManager seleMan2_;
113	<
114	<	};
104	>	int nPairs_;
105	>	};
106
107
108		}

Comparing trunk/src/applications/staticProps/RadialDistrFunc.hpp (property svn:keywords):
Revision 307 by tim, Wed Feb 9 18:12:47 2005 UTC vs.
Revision 2023 by gezelter, Thu Oct 2 14:35:14 2014 UTC

#	Line 0 | Line 1
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